Zarr group arg

install

@@ -129,6 +129,8 @@ install_command solve-intensities "net.preibisch.bigstitcher.spark.IntensitySolv
 install_command create-fusion-container "net.preibisch.bigstitcher.spark.CreateFusionContainer"
 install_command affine-fusion "net.preibisch.bigstitcher.spark.SparkAffineFusion"
 install_command nonrigid-fusion "net.preibisch.bigstitcher.spark.SparkNonRigidFusion"
+install_command create-dataset "net.preibisch.bigstitcher.spark.CreateDataset"
+install_command chain-commands "net.preibisch.bigstitcher.spark.ChainCommands"
 
 echo 'Installing utils ...'
 

pom.xml

@@ -103,7 +103,7 @@
 		<bigdataviewer-n5.version>1.0.2</bigdataviewer-n5.version>
 
 		<spim_data.version>2.3.5</spim_data.version>
-		<multiview-reconstruction.version>8.0.0</multiview-reconstruction.version>
+		<multiview-reconstruction.version>8.1.2-SNAPSHOT</multiview-reconstruction.version>
 		<BigStitcher.version>2.5.0</BigStitcher.version>
 
 		<n5-universe.version>2.3.0</n5-universe.version>

src/main/java/net/preibisch/bigstitcher/spark/ChainCommands.java

@@ -0,0 +1,129 @@
+package net.preibisch.bigstitcher.spark;
+
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.Stack;
+import java.util.concurrent.Callable;
+
+import mpicbg.spim.data.SpimDataException;
+import net.preibisch.bigstitcher.spark.abstractcmdline.AbstractInfrastructure;
+import picocli.CommandLine;
+
+public class ChainCommands extends AbstractInfrastructure implements Callable<Void>, Serializable
+{
+	private static final long serialVersionUID = 1584686229152127469L;
+
+	static class CommandWithArguments {
+		final List<String> cmdArgs;
+
+		CommandWithArguments(List<String> cmdArgs) {
+			this.cmdArgs = cmdArgs;
+		}
+	}
+
+	/**
+	 * Custom converter to collect all arguments after --command until a separator
+	 * (either ';' or '+') or the end of the input.
+	 */
+	static class CommandArgsConverter implements CommandLine.IParameterConsumer {
+		@Override
+		public void consumeParameters(Stack<String> args, CommandLine.Model.ArgSpec argSpec, CommandLine.Model.CommandSpec commandSpec) {
+			List<CommandWithArguments> currentCommands = argSpec.getValue();
+			List<String> commandArgs = new ArrayList<>();
+			while (!args.isEmpty()) {
+				String arg = args.pop();
+
+				if (";".equals(arg) || "+".equals(arg)) {
+					break;
+				}
+				if (arg.equals("-h") || arg.equals("--help")) {
+					// add back the help flag at the bottom of the stack
+					// but before check if there was anything left and if there wasn't stop after this
+					boolean done = args.isEmpty();
+					args.add(0, arg);
+					if (done) break;
+				} else
+					commandArgs.add(arg);
+			}
+			currentCommands.add(new CommandWithArguments(commandArgs));
+		}
+	}
+
+	@CommandLine.Option(names = { "-h", "--help" }, description = "display this help message", usageHelp = true)
+	boolean helpFlag;
+
+	@CommandLine.Option(names = { "--command" }, parameterConsumer = CommandArgsConverter.class,
+						description = "Command to execute with its arguments. Multiple commands can be chained using ';' or '+'.\n"
+									+ "Example: --command create-dataset --input-path /data/images/ --input-pattern '*.tif' ; "
+									+ "--command detect-interestpoints --detector SIFT --descriptor SIFT ; "
+									+ "--command match-interestpoints --matcher FLANN ; stitching --stitchingModel Affine")
+	List<CommandWithArguments> commands = new ArrayList<>();
+
+	@Override
+	public Void call() throws Exception {
+		for (CommandWithArguments commandArgs : commands) {
+			if (commandArgs.cmdArgs.isEmpty())
+				continue;
+
+			String cmdName = commandArgs.cmdArgs.get(0);
+			List<String> cmdArgs = new ArrayList<>(commandArgs.cmdArgs.subList(1, commandArgs.cmdArgs.size()));
+			addCommonOptions(cmdArgs);
+
+			AbstractInfrastructure cmdInstance = getCmdInstance(cmdName);
+			CommandLine currentCmdLine = new CommandLine(cmdInstance);
+			System.out.println("Execute command: " + cmdName + " with args: " + cmdArgs);
+			int exitCode = currentCmdLine.execute(cmdArgs.toArray(new String[0]));
+			if (exitCode != 0) {
+				System.err.println("Command " + cmdName + " failed with exit code " + exitCode);
+				System.exit(exitCode);
+			}
+		}
+		return null;
+	}
+
+	private AbstractInfrastructure getCmdInstance(String name) {
+		switch (name) {
+			case "clear-interestpoints": return new ClearInterestPoints();
+			case "clear-registrations": return new ClearRegistrations();
+			case "create-container": return new CreateFusionContainer();
+			case "detect-interestpoints": return new SparkInterestPointDetection();
+			case "match-interestpoints": return new SparkGeometricDescriptorMatching();
+			case "nonrigid-fusion": return new SparkNonRigidFusion();
+			case "create-dataset": return new CreateDataset();
+			case "stitching": return new SparkPairwiseStitching();
+			case "resave": return new SparkResaveN5();
+			case "downsample": return new SparkDownsample();
+			case "affine-fusion": return new SparkAffineFusion();
+			case "solver": return new Solver();
+			default: throw new IllegalArgumentException("Unknown command: " + name);
+		}
+	}
+
+	private void addCommonOptions(List<String> cmdArgs) {
+		if (this.dryRun) {
+			cmdArgs.add("--dryRun");
+		}
+		if (this.localSparkBindAddress) {
+			cmdArgs.add("--localSparkBindAddress");
+		}
+		if (this.s3Region != null && !this.s3Region.isEmpty()) {
+			cmdArgs.add("--s3Region");
+			cmdArgs.add(this.s3Region);
+		}
+	}
+
+	public static void main(final String... args) throws SpimDataException {
+		System.out.println(Arrays.toString(args));
+
+		ChainCommands chainedCommands = new ChainCommands();
+		CommandLine commandLine = new CommandLine(chainedCommands)
+				.setUnmatchedOptionsArePositionalParams(true)
+				;
+
+
+		System.exit(commandLine.execute(args));
+	}
+
+}

src/main/java/net/preibisch/bigstitcher/spark/Compressions.java

@@ -0,0 +1,5 @@
+package net.preibisch.bigstitcher.spark;
+
+public enum Compressions {
+	Lz4, Gzip, Zstandard, Blosc, Bzip2, Xz, Raw
+}

src/main/java/net/preibisch/bigstitcher/spark/CreateDataset.java

@@ -0,0 +1,68 @@
+package net.preibisch.bigstitcher.spark;
+
+import java.io.Serializable;
+import java.net.URI;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.Arrays;
+import java.util.concurrent.Callable;
+
+import mpicbg.spim.data.SpimDataException;
+import net.preibisch.bigstitcher.spark.abstractcmdline.AbstractBasic;
+import net.preibisch.mvrecon.dataset.SpimDatasetBuilder;
+import net.preibisch.mvrecon.fiji.spimdata.SpimData2;
+import net.preibisch.mvrecon.fiji.spimdata.XmlIoSpimData2;
+import picocli.CommandLine;
+import picocli.CommandLine.Option;
+import util.URITools;
+
+public class CreateDataset extends AbstractBasic implements Callable<Void>, Serializable
+{
+	private static final long serialVersionUID = -5155338208494730656L;
+
+	@Option(names = {"--input-path"}, required = true, description = "Path to the input images, e.g. /data/images/")
+	private String inputPath = "/Users/goinac/Work/HHMI/stitching/datasets/tiny_4_bigstitcher/t1/";
+
+	@Option(names = {"--input-pattern"}, description = "Glob pattern for input images, e.g. /data/images/*.tif")
+	private String inputPattern = "*";
+
+	@Override
+	public Void call() throws Exception {
+		this.setRegion();
+
+		SpimData2 spimData = createDataset();
+
+		URI xmlURI = URITools.toURI(xmlURIString);
+
+		System.out.println("Save spimData with original tiles to " + xmlURI);
+		prepareSaveLocation(xmlURI);
+		new XmlIoSpimData2().save(spimData, xmlURI);
+
+		return null;
+	}
+
+	private SpimData2 createDataset() {
+		SpimDatasetBuilder spimDatasetBuilder = new SpimDatasetBuilder(inputPattern);
+		return spimDatasetBuilder.createDataset(URITools.toURI(inputPath));
+	}
+
+	private void prepareSaveLocation(URI xmlURI) {
+		if (URITools.isFile( xmlURI )) {
+			Path xmlPath = Paths.get(xmlURI);
+			// create parent directories if necessary
+			if ( !xmlPath.getParent().toFile().exists() ) {
+				if (!xmlPath.getParent().toFile().mkdirs()) {
+					// log the error but continue
+					// if the directory wasn't create it will fail later when trying to write the file
+					System.out.println("Failed to create parent directory for " + xmlURI);
+				}
+			}
+		}
+	}
+
+	public static void main(final String... args) throws SpimDataException {
+		System.out.println(Arrays.toString(args));
+
+		System.exit(new CommandLine(new CreateDataset()).execute(args));
+	}
+}